• The tutorial for ioslides is here
• To render the slides to html and also extract the code chunks to a separate file, run from the command-line:

Rscript -e "rmarkdown::render('ioslide_template.Rmd'); knitr::knit('ioslide_template.Rmd', tangle=TRUE)"

• Shortcuts for different display modes
  • ‘f’: enable fullscreen mode
  • ‘w’: toggle widescreen mode
  • ‘o’: enable overview mode
  • ‘h’: enable code highlight mode
  • ‘p’: show presenter notes

\[f(k) = {n \choose k} p^{k} (1-p)^{n-k} \tag{1}\] \[\sigma_{M} = \frac{\sigma}{\sqrt(N)} \tag{2}\]

• Citations can be included autmatically by including them in BibTex format in file bibtex.bib and then citing the them in the text with this syntax [@refid1; @refid2]
• For example, the citation syntax [@Huber2015-ag; @Howard2013-fq] renders to: (Huber et al. 2015; Howard et al. 2013), and the corresponding references will then automatically be included at the end on a slide entitled ‘References’.
• More citations (Kim et al. 2013; Langmead and Salzberg 2012; Li and Durbin 2009; Li 2013; Liao, Smyth, and Shi 2013; Lawrence et al. 2013)

• Scrolling of code chunks supported by css code after preamble.

z <- "dajfdfkfffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff"
z
z
z
z
z
z
z
z
z

• Note: the print behavior of data.frames is autmatically paged when including df_print: paged in preamble. In addition, one can set how many rows are shown on each page by assigning the desired number to the rows.print argument in the header of the corresponding code chunk (e.g. below it is set to 75 rows).

x <- cbind(iris, iris[,5:1])
x

Print information about queues/partitions available on a cluster.

sinfo 

Compute jobs are submitted with sbatch via a submission script (here script_name.sh).

sbatch script_name.sh

Sample submission script

#!/bin/bash -l

#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=1G
#SBATCH --time=1-00:15:00 # 1 day and 15 minutes
#SBATCH --mail-user=useremail@address.com
#SBATCH --mail-type=ALL
#SBATCH --job-name="some_test"
#SBATCH -p batch # Choose queue/parition from: intel, batch, highmem, gpu, short

myscript.sh

Interactive session with specific resource requests

srun --x11 --partition=short --mem=2gb --cpus-per-task 4 --ntasks 1 --time 1:00:00 --pty bash -l

library(DT)
datatable(iris)

• Note: the default in ioslides uses larger font sizes where 'smaller: false' is used. You usually have it set to 'smaller: true'
• With default turned one can also set smaller font sizes on a per slide basis by specifying '{.smaller}' at the end of a slide title
• To have more fine control over font size use embedded HTML code. Here are some examples:
  • HTML font size 28px
  • HTML font size 18px
  • HTML font size 14px
  • HTML font size 12px

This can be useful to have a figure on the right and bullets describing it on the left.

• Bullet 1
• Bullet 2
• Bullet 3